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Action Replay can mess up your game by corrupting save files so they can't be accessed. basically you have to start a new game. or they can work just fine.

it all depends on the code in question because of what an AR actually does. Pokemon uses a hexidecimal system for its programming. so an AR changes the hex code of something to something else. usually you get more problems when you make drastic hex changes, like changing a Ninjasks ability to No Guard and teaching it Sheer Cold, as opposed to just teaching a Pokemon a move via TM that is normally only an Egg Move or Tutor Move. its hard to say 100% how the code in question will affect the game, since not too many people know the entire Hexidecimal spread for any given Pokemon game. hope that helps.

Its kinda use at your own risk.
if you've spent lots of time on your team, its probably not worth the risk. if you debt intend to play against anyone but your buds at home though, it can be fun to mess with people.